Dec

9

RNA-Seq Data Simulator

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The FLUX SIMULATOR

The FluxSimulator is the part of the FLUX project that aims at providing an in silico reproduction of the experimental pipelines for RNA-Seq, adopting a minimal set of parameters. Corresponding models were established after analyzing RNA-Seq experiments from different cell types, sample preparation protocols and sequencing platforms. The first step of the FLUX project is-in fact-a transcriptome simulator. Subsequently, common sources of systematic bias in the abundance and distribution of produced reads are mimicked-whether they incur during library construction, or, in the sequencing process. The FluxSimulator provides a flexible base to design benchmark experiments based on the new sequencing technologies, as for instance abundance predictions of the FluxCapacitor.

Availability

The FluxSimulator is available following the links from the download page. It provides a command line interface for batch mode, as well as a graphical user interface for introspection of each step while being carried out. Sample files are provided with the correspondingly marked download bundles.

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Comments

One Response to “RNA-Seq Data Simulator”

  1. Jim Silverton on January 11th, 2011 9:13 pm

    I am interested in simulating two types of data using R:

    (1) SNP data and
    (2) RNA seq data

    I would like to simulate the data where say 40% of the data comes from the true null distribution.
    For the RNA seq data, I would like to simulate like to simulate data using the same 40% from the null but the data has the following look:

    Control Treatment
    2 4
    2 5
    4 4
    1 0
    3 1

    etc. Each row represents a gene and we would like to do a Fisher’s exact test for each gene.
    I am using R. If there is a practical way of doing this instead of using software, I will appreciate it.

    Thanks

    Jim

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